AMBER Archive (2006)

Subject: AMBER: RE: Intel Compiler.

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue May 09 2006 - 11:05:28 CDT

Dear Priti

>export TESTsander=/software/amebr9/exe/sander.MPI; make test.sander.BASIC

Is the amebr9 in the error message here a typo in the email or the real
message? I suspect that you may have a typo in your definition of AMBERHOME.
Try:

echo $AMBERHOME

Does it show /software/amebr9 or /software/amber9

If it points to the wrong path correct it, then logout and try logging back
in and running the test again.

Alternatively if it was simply a typo in the email then the error may be due
to the fact that some nodes can't see the executable. When running in
parallel 'ALL' nodes need to be able to see the executable in the 'SAME'
place. I.e. you will likely have to make sure that the executable directory
is on an NFS path that is mounted by all nodes.

All the best
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

> -----Original Message-----
> From: Priti Hansia [mailto:priti_at_mbu.iisc.ernet.in]
> Sent: Tuesday, May 09, 2006 08:57
> To: Ross Walker
> Subject: RE: Intel Compiler.
>
>
> Thanks Ross. I would do that.
>
> Following is the error I got while testing parallel version:
>
> [root_at_genomics test]# make test.parallel
> export TESTsander=/software/amebr9/exe/sander.MPI; make
> test.sander.BASIC
> make[1]: Entering directory `/software/amber9/test'
> cd dmp; ./Run.dmp
> /software/amebr9/exe/sander.MPI: Command not found.
> ./Run.dmp: Program error
> make[1]: *** [test.sander.BASIC] Error 1
> make[1]: Leaving directory `/software/amber9/test'
> make: *** [test.sander.BASIC.MPI] Error 2
>
> I have checked that 'sander.MPI' IS there in
> /software/amber9/exe path.
> But I dont know why it says '/software/amebr9/exe/sander.MPI:
> Command not
> found' !
>
> Regards,
> -Priti
>
>
>
> > Hi Priti,
> >
> > What was the error you saw? I haven't seen the message turn
> up yet on the
> > mailing list. I am glad you got it working in serial though.
> >
> > This is fine, don't worry about that. I just didn't want it
> getting around
> > that I used my premier account to give you the file since I have a
> > developers account with Intel and they wouldn't be very
> happy. But yes
> > feel free to hand that file around and just tell people you
> logged into
> > premier.intel.com to get it.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | HPC Consultant and Staff Scientist |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on request |
> >
> > Note: Electronic Mail is not secure, has no guarantee of
> delivery, may not
> > be read every day, and should not be used for urgent or
> sensitive issues.
> >
> >
> >
>
>

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